Starting phenix.real_space_refine on Sat Aug 23 14:52:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dd6_30645/08_2025/7dd6_30645.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dd6_30645/08_2025/7dd6_30645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dd6_30645/08_2025/7dd6_30645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dd6_30645/08_2025/7dd6_30645.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dd6_30645/08_2025/7dd6_30645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dd6_30645/08_2025/7dd6_30645.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 70 5.16 5 Cl 2 4.86 5 C 8213 2.51 5 N 2028 2.21 5 O 2359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12678 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6209 Classifications: {'peptide': 791} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PTRANS': 34, 'TRANS': 756} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 6235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6235 Classifications: {'peptide': 792} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 33, 'TRANS': 758} Chain breaks: 3 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Unusual residues: {' CA': 3, ' CL': 1, 'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Unusual residues: {' CA': 3, ' CL': 1, 'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.85, per 1000 atoms: 0.22 Number of scatterers: 12678 At special positions: 0 Unit cell: (100.386, 93.288, 182.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 Cl 2 17.00 S 70 16.00 O 2359 8.00 N 2028 7.00 C 8213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.73 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 448 " distance=2.24 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 545 " - pdb=" SG CYS A 564 " distance=2.04 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 581 " distance=2.03 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 597 " distance=2.49 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS A 764 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 561 " distance=2.66 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 597 " distance=1.82 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 764 " distance=2.39 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1105 " - " ASN A 287 " " NAG A1106 " - " ASN A 399 " " NAG A1107 " - " ASN A 467 " " NAG B1105 " - " ASN B 287 " " NAG B1106 " - " ASN B 399 " " NAG B1107 " - " ASN B 467 " " NAG C 1 " - " ASN A 487 " " NAG D 1 " - " ASN A 540 " " NAG E 1 " - " ASN B 487 " " NAG F 1 " - " ASN B 540 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 500.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 16 sheets defined 49.5% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.641A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.712A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.707A pdb=" N LEU A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.561A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 307 through 315 removed outlier: 4.387A pdb=" N VAL A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 399 through 403 removed outlier: 3.780A pdb=" N VAL A 403 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 435 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.594A pdb=" N LYS A 453 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 454 " --> pdb=" O ILE A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 454' Processing helix chain 'A' and resid 455 through 465 removed outlier: 3.526A pdb=" N HIS A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 609 through 636 Processing helix chain 'A' and resid 639 through 644 removed outlier: 4.209A pdb=" N LYS A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 663 Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.557A pdb=" N ILE A 668 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 697 removed outlier: 3.577A pdb=" N CYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Proline residue: A 681 - end of helix Processing helix chain 'A' and resid 700 through 706 Processing helix chain 'A' and resid 720 through 745 removed outlier: 3.605A pdb=" N LEU A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE A 732 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 792 Processing helix chain 'A' and resid 801 through 826 removed outlier: 4.163A pdb=" N PHE A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Proline residue: A 822 - end of helix removed outlier: 3.552A pdb=" N SER A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 862 removed outlier: 3.798A pdb=" N SER A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN A 854 " --> pdb=" O CYS A 850 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS A 855 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.728A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 146 through 158 removed outlier: 4.027A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.643A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.530A pdb=" N ALA B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.913A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 296 through 301 removed outlier: 4.501A pdb=" N SER B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.703A pdb=" N ARG B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.733A pdb=" N PHE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 415 through 435 Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 450 through 454 removed outlier: 3.621A pdb=" N LYS B 453 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 454 " --> pdb=" O ILE B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 450 through 454' Processing helix chain 'B' and resid 455 through 465 removed outlier: 3.617A pdb=" N HIS B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 636 Processing helix chain 'B' and resid 639 through 644 removed outlier: 4.097A pdb=" N LYS B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 663 Processing helix chain 'B' and resid 664 through 668 removed outlier: 3.626A pdb=" N ILE B 668 " --> pdb=" O LEU B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 697 Proline residue: B 681 - end of helix Processing helix chain 'B' and resid 700 through 706 Processing helix chain 'B' and resid 720 through 743 removed outlier: 4.080A pdb=" N PHE B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 727 " --> pdb=" O GLN B 723 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE B 732 " --> pdb=" O PHE B 728 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 737 " --> pdb=" O VAL B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 793 removed outlier: 3.603A pdb=" N SER B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 removed outlier: 3.978A pdb=" N PHE B 805 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Proline residue: B 822 - end of helix Processing helix chain 'B' and resid 828 through 862 removed outlier: 3.615A pdb=" N SER B 833 " --> pdb=" O GLY B 829 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN B 854 " --> pdb=" O CYS B 850 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LYS B 855 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.103A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.819A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.983A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 320 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N THR A 317 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 488 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N HIS A 509 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 490 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA5, first strand: chain 'A' and resid 549 through 553 Processing sheet with id=AA6, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AA7, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA8, first strand: chain 'A' and resid 601 through 603 removed outlier: 6.751A pdb=" N GLN A 601 " --> pdb=" O ILE A 760 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ILE A 762 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU A 603 " --> pdb=" O ILE A 762 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N CYS A 764 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.971A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE B 33 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N VAL B 142 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY B 35 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.849A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.919A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TRP B 208 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N VAL B 268 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TRP B 293 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE B 320 " --> pdb=" O TRP B 293 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA B 295 " --> pdb=" O PHE B 320 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR B 317 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR B 488 " --> pdb=" O HIS B 509 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N HIS B 509 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 490 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 469 Processing sheet with id=AB4, first strand: chain 'B' and resid 549 through 552 Processing sheet with id=AB5, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AB6, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB7, first strand: chain 'B' and resid 601 through 603 removed outlier: 4.117A pdb=" N ILE B 762 " --> pdb=" O GLU B 603 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2054 1.31 - 1.44: 3635 1.44 - 1.57: 7216 1.57 - 1.70: 0 1.70 - 1.83: 86 Bond restraints: 12991 Sorted by residual: bond pdb=" C7 NAG A1107 " pdb=" N2 NAG A1107 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C7 NAG B1105 " pdb=" N2 NAG B1105 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C7 NAG B1106 " pdb=" N2 NAG B1106 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C7 NAG B1107 " pdb=" N2 NAG B1107 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C7 NAG F 1 " pdb=" N2 NAG F 1 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 12986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 17096 2.03 - 4.07: 443 4.07 - 6.10: 81 6.10 - 8.14: 17 8.14 - 10.17: 4 Bond angle restraints: 17641 Sorted by residual: angle pdb=" C THR B 698 " pdb=" N ASN B 699 " pdb=" CA ASN B 699 " ideal model delta sigma weight residual 120.71 127.74 -7.03 1.42e+00 4.96e-01 2.45e+01 angle pdb=" C ILE B 740 " pdb=" N TRP B 741 " pdb=" CA TRP B 741 " ideal model delta sigma weight residual 120.28 114.96 5.32 1.34e+00 5.57e-01 1.58e+01 angle pdb=" CA ARG B 700 " pdb=" C ARG B 700 " pdb=" O ARG B 700 " ideal model delta sigma weight residual 122.44 117.38 5.06 1.34e+00 5.57e-01 1.42e+01 angle pdb=" CA ARG A 700 " pdb=" C ARG A 700 " pdb=" O ARG A 700 " ideal model delta sigma weight residual 122.44 117.39 5.05 1.34e+00 5.57e-01 1.42e+01 angle pdb=" N LYS A 697 " pdb=" CA LYS A 697 " pdb=" C LYS A 697 " ideal model delta sigma weight residual 113.21 109.06 4.15 1.15e+00 7.56e-01 1.30e+01 ... (remaining 17636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 7193 23.36 - 46.72: 510 46.72 - 70.08: 89 70.08 - 93.44: 30 93.44 - 116.80: 7 Dihedral angle restraints: 7829 sinusoidal: 3225 harmonic: 4604 Sorted by residual: dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 448 " pdb=" CB CYS B 448 " ideal model delta sinusoidal sigma weight residual 93.00 -178.39 -88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B 676 " pdb=" SG CYS B 676 " pdb=" SG CYS B 764 " pdb=" CB CYS B 764 " ideal model delta sinusoidal sigma weight residual 93.00 7.40 85.60 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS B 541 " pdb=" SG CYS B 541 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual 93.00 16.54 76.46 1 1.00e+01 1.00e-02 7.35e+01 ... (remaining 7826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1921 0.105 - 0.210: 80 0.210 - 0.315: 3 0.315 - 0.420: 0 0.420 - 0.525: 1 Chirality restraints: 2005 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 7.78e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 487 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" CA VAL A 704 " pdb=" N VAL A 704 " pdb=" C VAL A 704 " pdb=" CB VAL A 704 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2002 not shown) Planarity restraints: 2239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 697 " 0.024 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C LYS B 697 " -0.082 2.00e-02 2.50e+03 pdb=" O LYS B 697 " 0.031 2.00e-02 2.50e+03 pdb=" N THR B 698 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 670 " -0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO B 671 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 671 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 671 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 187 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 188 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.024 5.00e-02 4.00e+02 ... (remaining 2236 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 374 2.68 - 3.24: 13018 3.24 - 3.79: 19599 3.79 - 4.35: 25818 4.35 - 4.90: 42025 Nonbonded interactions: 100834 Sorted by model distance: nonbonded pdb=" O LEU B 430 " pdb=" CG2 ILE B 433 " model vdw 2.126 3.460 nonbonded pdb=" O ILE B 623 " pdb=" OG1 THR B 626 " model vdw 2.147 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O TRP B1108 " model vdw 2.153 3.040 nonbonded pdb=" O ALA A 110 " pdb=" OG SER A 113 " model vdw 2.187 3.040 nonbonded pdb=" OG SER B 150 " pdb=" OG SER B 169 " model vdw 2.192 3.040 ... (remaining 100829 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 119 or resid 136 through 1108)) selection = (chain 'B' and (resid 22 through 119 or resid 136 through 358 or (resid 359 and \ (name N or name CA or name C or name O or name CB )) or resid 392 through 1108)) \ } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.450 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.701 13022 Z= 0.664 Angle : 1.056 49.632 17717 Z= 0.552 Chirality : 0.050 0.525 2005 Planarity : 0.004 0.051 2229 Dihedral : 16.894 116.801 4798 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.07 % Allowed : 20.34 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.18), residues: 1567 helix: -1.20 (0.17), residues: 685 sheet: -2.17 (0.37), residues: 153 loop : -2.84 (0.18), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 677 TYR 0.014 0.001 TYR A 750 PHE 0.015 0.001 PHE B 562 TRP 0.010 0.001 TRP A 299 HIS 0.004 0.001 HIS B 765 Details of bonding type rmsd covalent geometry : bond 0.00829 (12991) covalent geometry : angle 0.80855 (17641) SS BOND : bond 0.27788 ( 17) SS BOND : angle 15.19897 ( 34) hydrogen bonds : bond 0.13911 ( 594) hydrogen bonds : angle 6.70983 ( 1722) link_BETA1-4 : bond 0.00479 ( 4) link_BETA1-4 : angle 1.05161 ( 12) link_NAG-ASN : bond 0.00406 ( 10) link_NAG-ASN : angle 3.51666 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.9125 (tp) cc_final: 0.8882 (tt) REVERT: A 571 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7217 (mt-10) REVERT: A 587 ASP cc_start: 0.8364 (p0) cc_final: 0.7842 (t0) REVERT: A 756 GLU cc_start: 0.7753 (tp30) cc_final: 0.7148 (tp30) REVERT: A 810 MET cc_start: 0.6302 (mtm) cc_final: 0.5673 (mtm) REVERT: A 813 PHE cc_start: 0.6804 (t80) cc_final: 0.6536 (t80) REVERT: B 472 MET cc_start: 0.8335 (mtm) cc_final: 0.8129 (mtm) REVERT: B 752 ASN cc_start: 0.8592 (t0) cc_final: 0.8191 (m110) REVERT: B 787 PHE cc_start: 0.7982 (t80) cc_final: 0.7728 (t80) REVERT: B 800 PHE cc_start: 0.8809 (m-10) cc_final: 0.8290 (m-80) REVERT: B 805 PHE cc_start: 0.8393 (m-80) cc_final: 0.7817 (m-80) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.0991 time to fit residues: 28.0053 Evaluate side-chains 105 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 741 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 335 GLN A 465 HIS ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN A 734 GLN A 752 ASN A 799 ASN B 23 ASN B 118 ASN B 193 GLN B 245 GLN B 260 GLN B 335 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS B 494 HIS B 509 HIS B 734 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.125834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.083730 restraints weight = 26813.105| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.25 r_work: 0.3172 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13022 Z= 0.167 Angle : 0.706 15.486 17717 Z= 0.348 Chirality : 0.049 0.718 2005 Planarity : 0.005 0.062 2229 Dihedral : 9.421 109.497 1975 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.34 % Allowed : 20.49 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.20), residues: 1567 helix: 0.07 (0.19), residues: 708 sheet: -1.56 (0.38), residues: 175 loop : -2.25 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 265 TYR 0.014 0.001 TYR B 651 PHE 0.039 0.002 PHE A 814 TRP 0.015 0.001 TRP B 674 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00371 (12991) covalent geometry : angle 0.68298 (17641) SS BOND : bond 0.00539 ( 17) SS BOND : angle 1.48957 ( 34) hydrogen bonds : bond 0.05538 ( 594) hydrogen bonds : angle 5.14480 ( 1722) link_BETA1-4 : bond 0.00486 ( 4) link_BETA1-4 : angle 1.56083 ( 12) link_NAG-ASN : bond 0.00456 ( 10) link_NAG-ASN : angle 4.02224 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.358 Fit side-chains REVERT: A 528 LEU cc_start: 0.9085 (tp) cc_final: 0.8696 (tt) REVERT: A 587 ASP cc_start: 0.8872 (p0) cc_final: 0.8234 (t0) REVERT: A 641 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6208 (mt) REVERT: A 751 ARG cc_start: 0.7416 (ptm160) cc_final: 0.6458 (ptm160) REVERT: A 752 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8181 (t0) REVERT: A 756 GLU cc_start: 0.7978 (tp30) cc_final: 0.7263 (tp30) REVERT: A 810 MET cc_start: 0.5917 (mtm) cc_final: 0.5599 (mtm) REVERT: A 845 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: B 462 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.7891 (m170) REVERT: B 787 PHE cc_start: 0.8119 (t80) cc_final: 0.7826 (t80) outliers start: 45 outliers final: 19 residues processed: 149 average time/residue: 0.0800 time to fit residues: 19.1343 Evaluate side-chains 116 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 15 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 71 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 594 HIS A 752 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.124340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082404 restraints weight = 27204.708| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.08 r_work: 0.3196 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13022 Z= 0.180 Angle : 0.653 16.669 17717 Z= 0.322 Chirality : 0.048 0.696 2005 Planarity : 0.004 0.065 2229 Dihedral : 7.909 108.395 1973 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.56 % Allowed : 20.34 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.20), residues: 1567 helix: 0.56 (0.19), residues: 704 sheet: -1.24 (0.39), residues: 175 loop : -2.04 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 751 TYR 0.012 0.001 TYR B 417 PHE 0.030 0.001 PHE A 788 TRP 0.012 0.001 TRP A 299 HIS 0.004 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00405 (12991) covalent geometry : angle 0.62716 (17641) SS BOND : bond 0.00378 ( 17) SS BOND : angle 1.14972 ( 34) hydrogen bonds : bond 0.05198 ( 594) hydrogen bonds : angle 4.91904 ( 1722) link_BETA1-4 : bond 0.00327 ( 4) link_BETA1-4 : angle 1.56144 ( 12) link_NAG-ASN : bond 0.00348 ( 10) link_NAG-ASN : angle 4.23764 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 0.371 Fit side-chains REVERT: A 587 ASP cc_start: 0.8557 (p0) cc_final: 0.7984 (t0) REVERT: A 641 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6464 (mt) REVERT: A 756 GLU cc_start: 0.7950 (tp30) cc_final: 0.7387 (tp30) REVERT: A 810 MET cc_start: 0.5999 (mtm) cc_final: 0.5737 (mtm) REVERT: A 814 PHE cc_start: 0.8057 (m-80) cc_final: 0.7752 (m-80) REVERT: A 845 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: B 307 MET cc_start: 0.8083 (mtp) cc_final: 0.7597 (mtt) REVERT: B 604 PHE cc_start: 0.7456 (p90) cc_final: 0.6900 (p90) outliers start: 48 outliers final: 25 residues processed: 137 average time/residue: 0.0667 time to fit residues: 15.0253 Evaluate side-chains 121 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.123645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.082172 restraints weight = 26987.432| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.04 r_work: 0.3203 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13022 Z= 0.169 Angle : 0.641 16.538 17717 Z= 0.310 Chirality : 0.048 0.709 2005 Planarity : 0.004 0.065 2229 Dihedral : 7.521 107.173 1973 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.86 % Allowed : 21.83 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.21), residues: 1567 helix: 0.86 (0.19), residues: 707 sheet: -0.87 (0.42), residues: 164 loop : -1.83 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 54 TYR 0.011 0.001 TYR B 417 PHE 0.016 0.001 PHE B 633 TRP 0.011 0.001 TRP A 299 HIS 0.003 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00384 (12991) covalent geometry : angle 0.61767 (17641) SS BOND : bond 0.00341 ( 17) SS BOND : angle 1.16809 ( 34) hydrogen bonds : bond 0.04897 ( 594) hydrogen bonds : angle 4.74057 ( 1722) link_BETA1-4 : bond 0.00317 ( 4) link_BETA1-4 : angle 1.57794 ( 12) link_NAG-ASN : bond 0.00329 ( 10) link_NAG-ASN : angle 3.93698 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 96 time to evaluate : 0.496 Fit side-chains REVERT: A 223 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7681 (tp) REVERT: A 229 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 587 ASP cc_start: 0.8537 (p0) cc_final: 0.7989 (t0) REVERT: A 741 TRP cc_start: 0.7693 (OUTLIER) cc_final: 0.7091 (m100) REVERT: A 751 ARG cc_start: 0.8422 (mtp180) cc_final: 0.8159 (mmm-85) REVERT: A 756 GLU cc_start: 0.7848 (tp30) cc_final: 0.7274 (tp30) REVERT: A 845 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: B 307 MET cc_start: 0.8177 (mtp) cc_final: 0.7676 (mtt) REVERT: B 725 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7966 (mt) REVERT: B 751 ARG cc_start: 0.9255 (mtp85) cc_final: 0.9025 (mtp85) REVERT: B 770 MET cc_start: 0.5655 (mmm) cc_final: 0.5336 (mmm) outliers start: 52 outliers final: 28 residues processed: 140 average time/residue: 0.0805 time to fit residues: 18.3005 Evaluate side-chains 122 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 150 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.122116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.080079 restraints weight = 27207.016| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.04 r_work: 0.3167 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 13022 Z= 0.216 Angle : 0.667 17.617 17717 Z= 0.325 Chirality : 0.049 0.723 2005 Planarity : 0.004 0.068 2229 Dihedral : 7.502 107.115 1973 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.93 % Allowed : 21.83 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.20), residues: 1567 helix: 0.91 (0.19), residues: 704 sheet: -1.06 (0.39), residues: 184 loop : -1.74 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 54 TYR 0.012 0.001 TYR B 417 PHE 0.018 0.001 PHE B 788 TRP 0.012 0.001 TRP B 674 HIS 0.004 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00503 (12991) covalent geometry : angle 0.64300 (17641) SS BOND : bond 0.00472 ( 17) SS BOND : angle 1.12170 ( 34) hydrogen bonds : bond 0.05131 ( 594) hydrogen bonds : angle 4.71520 ( 1722) link_BETA1-4 : bond 0.00195 ( 4) link_BETA1-4 : angle 1.64366 ( 12) link_NAG-ASN : bond 0.00297 ( 10) link_NAG-ASN : angle 4.12281 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 98 time to evaluate : 0.347 Fit side-chains REVERT: A 587 ASP cc_start: 0.8609 (p0) cc_final: 0.8083 (t0) REVERT: A 751 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7974 (mmm-85) REVERT: A 752 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.7354 (p0) REVERT: A 756 GLU cc_start: 0.7931 (tp30) cc_final: 0.7369 (tp30) REVERT: A 845 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: B 307 MET cc_start: 0.8268 (mtp) cc_final: 0.7816 (mtt) REVERT: B 698 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7960 (p) REVERT: B 725 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8013 (mt) outliers start: 53 outliers final: 36 residues processed: 138 average time/residue: 0.0799 time to fit residues: 17.6354 Evaluate side-chains 129 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN B 335 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.121927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079759 restraints weight = 27033.900| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.03 r_work: 0.3154 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13022 Z= 0.217 Angle : 0.660 17.287 17717 Z= 0.321 Chirality : 0.049 0.724 2005 Planarity : 0.004 0.069 2229 Dihedral : 7.497 107.406 1973 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.53 % Allowed : 22.20 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.21), residues: 1567 helix: 0.96 (0.19), residues: 704 sheet: -1.28 (0.37), residues: 193 loop : -1.66 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.011 0.001 TYR B 417 PHE 0.014 0.001 PHE B 788 TRP 0.010 0.001 TRP A 299 HIS 0.003 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00506 (12991) covalent geometry : angle 0.63682 (17641) SS BOND : bond 0.00385 ( 17) SS BOND : angle 1.16154 ( 34) hydrogen bonds : bond 0.05015 ( 594) hydrogen bonds : angle 4.65908 ( 1722) link_BETA1-4 : bond 0.00190 ( 4) link_BETA1-4 : angle 1.65015 ( 12) link_NAG-ASN : bond 0.00301 ( 10) link_NAG-ASN : angle 4.05775 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 91 time to evaluate : 0.404 Fit side-chains REVERT: A 528 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8619 (tt) REVERT: A 587 ASP cc_start: 0.8699 (p0) cc_final: 0.8063 (t0) REVERT: A 751 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8063 (mmm-85) REVERT: A 752 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8287 (t0) REVERT: A 756 GLU cc_start: 0.8013 (tp30) cc_final: 0.7372 (tp30) REVERT: A 808 PHE cc_start: 0.8233 (m-80) cc_final: 0.8032 (m-80) REVERT: A 810 MET cc_start: 0.6316 (mtm) cc_final: 0.5833 (mtm) REVERT: A 814 PHE cc_start: 0.8041 (m-80) cc_final: 0.7690 (m-80) REVERT: A 845 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: B 307 MET cc_start: 0.8250 (mtp) cc_final: 0.7785 (mtt) REVERT: B 571 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: B 725 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8041 (mt) outliers start: 61 outliers final: 41 residues processed: 139 average time/residue: 0.0712 time to fit residues: 15.9668 Evaluate side-chains 135 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 88 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN B 338 HIS ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.122412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.080443 restraints weight = 27015.989| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.02 r_work: 0.3164 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13022 Z= 0.188 Angle : 0.655 16.819 17717 Z= 0.315 Chirality : 0.049 0.713 2005 Planarity : 0.004 0.063 2229 Dihedral : 7.447 106.779 1973 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.23 % Allowed : 22.94 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.21), residues: 1567 helix: 1.06 (0.19), residues: 704 sheet: -1.07 (0.38), residues: 185 loop : -1.62 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 751 TYR 0.010 0.001 TYR B 417 PHE 0.015 0.001 PHE B 852 TRP 0.011 0.001 TRP B 299 HIS 0.003 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00437 (12991) covalent geometry : angle 0.62995 (17641) SS BOND : bond 0.00363 ( 17) SS BOND : angle 1.66505 ( 34) hydrogen bonds : bond 0.04822 ( 594) hydrogen bonds : angle 4.57892 ( 1722) link_BETA1-4 : bond 0.00177 ( 4) link_BETA1-4 : angle 1.62380 ( 12) link_NAG-ASN : bond 0.00297 ( 10) link_NAG-ASN : angle 3.93312 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 91 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 528 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8630 (tt) REVERT: A 587 ASP cc_start: 0.8611 (p0) cc_final: 0.7955 (t0) REVERT: A 751 ARG cc_start: 0.8367 (mtp180) cc_final: 0.8040 (mmm-85) REVERT: A 752 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8366 (t0) REVERT: A 756 GLU cc_start: 0.7970 (tp30) cc_final: 0.7217 (tp30) REVERT: A 810 MET cc_start: 0.6267 (mtm) cc_final: 0.5789 (mtt) REVERT: A 814 PHE cc_start: 0.8060 (m-80) cc_final: 0.7692 (m-80) REVERT: A 845 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: B 307 MET cc_start: 0.8230 (mtp) cc_final: 0.7788 (mtt) REVERT: B 571 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: B 698 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8177 (p) REVERT: B 725 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7977 (mt) outliers start: 57 outliers final: 41 residues processed: 138 average time/residue: 0.0716 time to fit residues: 16.2753 Evaluate side-chains 135 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 88 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 56 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN B 492 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.121553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.079868 restraints weight = 26661.191| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.98 r_work: 0.3139 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13022 Z= 0.223 Angle : 0.675 17.198 17717 Z= 0.327 Chirality : 0.050 0.719 2005 Planarity : 0.004 0.060 2229 Dihedral : 7.518 107.201 1973 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.45 % Allowed : 22.64 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.21), residues: 1567 helix: 1.09 (0.19), residues: 702 sheet: -1.22 (0.38), residues: 187 loop : -1.60 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 751 TYR 0.011 0.001 TYR B 203 PHE 0.016 0.001 PHE B 852 TRP 0.010 0.001 TRP A 299 HIS 0.004 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00520 (12991) covalent geometry : angle 0.65179 (17641) SS BOND : bond 0.00373 ( 17) SS BOND : angle 1.49161 ( 34) hydrogen bonds : bond 0.04993 ( 594) hydrogen bonds : angle 4.60503 ( 1722) link_BETA1-4 : bond 0.00176 ( 4) link_BETA1-4 : angle 1.66546 ( 12) link_NAG-ASN : bond 0.00311 ( 10) link_NAG-ASN : angle 3.96373 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 87 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 528 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8636 (tt) REVERT: A 587 ASP cc_start: 0.8518 (p0) cc_final: 0.7835 (t0) REVERT: A 751 ARG cc_start: 0.8394 (mtp180) cc_final: 0.8025 (mmm-85) REVERT: A 752 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8183 (t0) REVERT: A 756 GLU cc_start: 0.7949 (tp30) cc_final: 0.7130 (tp30) REVERT: A 810 MET cc_start: 0.6289 (mtm) cc_final: 0.5764 (mtm) REVERT: A 814 PHE cc_start: 0.7989 (m-80) cc_final: 0.7661 (m-80) REVERT: B 307 MET cc_start: 0.8262 (mtp) cc_final: 0.7832 (mtt) REVERT: B 571 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: B 698 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 725 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8010 (mt) outliers start: 60 outliers final: 45 residues processed: 135 average time/residue: 0.0846 time to fit residues: 18.7246 Evaluate side-chains 135 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 85 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 753 HIS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 44 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 34 optimal weight: 0.0010 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 335 GLN B 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.123067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.081706 restraints weight = 26710.528| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.04 r_work: 0.3138 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13022 Z= 0.158 Angle : 0.636 16.951 17717 Z= 0.304 Chirality : 0.048 0.707 2005 Planarity : 0.004 0.059 2229 Dihedral : 7.343 105.943 1973 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.79 % Allowed : 23.39 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.21), residues: 1567 helix: 1.19 (0.19), residues: 701 sheet: -1.16 (0.38), residues: 187 loop : -1.51 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 751 TYR 0.011 0.001 TYR B 824 PHE 0.024 0.001 PHE B 820 TRP 0.012 0.001 TRP B 299 HIS 0.002 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00363 (12991) covalent geometry : angle 0.61298 (17641) SS BOND : bond 0.00331 ( 17) SS BOND : angle 1.37112 ( 34) hydrogen bonds : bond 0.04582 ( 594) hydrogen bonds : angle 4.48286 ( 1722) link_BETA1-4 : bond 0.00257 ( 4) link_BETA1-4 : angle 1.57047 ( 12) link_NAG-ASN : bond 0.00262 ( 10) link_NAG-ASN : angle 3.83251 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 84 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 528 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8625 (tt) REVERT: A 587 ASP cc_start: 0.8620 (p0) cc_final: 0.7903 (t0) REVERT: A 751 ARG cc_start: 0.8376 (mtp180) cc_final: 0.8005 (mmm-85) REVERT: A 752 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8216 (t0) REVERT: A 756 GLU cc_start: 0.7927 (tp30) cc_final: 0.7120 (tp30) REVERT: A 810 MET cc_start: 0.6292 (mtm) cc_final: 0.5730 (mtm) REVERT: A 814 PHE cc_start: 0.7974 (m-80) cc_final: 0.7624 (m-80) REVERT: B 307 MET cc_start: 0.8226 (mtp) cc_final: 0.7796 (mtt) REVERT: B 571 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: B 698 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8207 (p) REVERT: B 725 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7999 (mt) outliers start: 51 outliers final: 38 residues processed: 127 average time/residue: 0.0819 time to fit residues: 17.0752 Evaluate side-chains 126 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 83 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 chunk 38 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 109 optimal weight: 0.0030 chunk 130 optimal weight: 10.0000 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.123102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.081823 restraints weight = 27059.448| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.90 r_work: 0.3193 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13022 Z= 0.162 Angle : 0.640 17.492 17717 Z= 0.305 Chirality : 0.048 0.701 2005 Planarity : 0.004 0.058 2229 Dihedral : 7.298 105.290 1973 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.19 % Allowed : 23.83 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.21), residues: 1567 helix: 1.23 (0.19), residues: 701 sheet: -1.09 (0.38), residues: 185 loop : -1.42 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 751 TYR 0.012 0.001 TYR A 824 PHE 0.024 0.001 PHE B 618 TRP 0.011 0.001 TRP B 299 HIS 0.003 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00373 (12991) covalent geometry : angle 0.61803 (17641) SS BOND : bond 0.00300 ( 17) SS BOND : angle 1.33760 ( 34) hydrogen bonds : bond 0.04582 ( 594) hydrogen bonds : angle 4.46534 ( 1722) link_BETA1-4 : bond 0.00192 ( 4) link_BETA1-4 : angle 1.61026 ( 12) link_NAG-ASN : bond 0.00273 ( 10) link_NAG-ASN : angle 3.80001 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 83 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8428 (tm-30) REVERT: A 528 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8609 (tt) REVERT: A 752 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8140 (t0) REVERT: A 756 GLU cc_start: 0.7951 (tp30) cc_final: 0.7143 (tp30) REVERT: A 810 MET cc_start: 0.6305 (mtm) cc_final: 0.5776 (mtm) REVERT: A 814 PHE cc_start: 0.7999 (m-80) cc_final: 0.7638 (m-80) REVERT: B 307 MET cc_start: 0.8202 (mtp) cc_final: 0.7756 (mtt) REVERT: B 571 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: B 698 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8251 (p) REVERT: B 725 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8065 (mt) outliers start: 43 outliers final: 35 residues processed: 121 average time/residue: 0.0682 time to fit residues: 13.7232 Evaluate side-chains 122 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 82 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 153 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.123871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.082548 restraints weight = 26784.211| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.91 r_work: 0.3150 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13022 Z= 0.140 Angle : 0.620 15.920 17717 Z= 0.295 Chirality : 0.047 0.690 2005 Planarity : 0.004 0.057 2229 Dihedral : 7.190 104.207 1973 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.04 % Allowed : 24.05 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.21), residues: 1567 helix: 1.30 (0.19), residues: 699 sheet: -1.04 (0.38), residues: 185 loop : -1.35 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 751 TYR 0.011 0.001 TYR A 824 PHE 0.021 0.001 PHE B 618 TRP 0.012 0.001 TRP B 299 HIS 0.002 0.000 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00320 (12991) covalent geometry : angle 0.59894 (17641) SS BOND : bond 0.00294 ( 17) SS BOND : angle 1.22289 ( 34) hydrogen bonds : bond 0.04366 ( 594) hydrogen bonds : angle 4.40476 ( 1722) link_BETA1-4 : bond 0.00300 ( 4) link_BETA1-4 : angle 1.58996 ( 12) link_NAG-ASN : bond 0.00287 ( 10) link_NAG-ASN : angle 3.70306 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2989.48 seconds wall clock time: 51 minutes 51.77 seconds (3111.77 seconds total)